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Escherichia coli (E. coli) Is a Model Bacterium

Escherichia coli (E. coli) Is a Model Bacterium

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Cell wall

FIGURE 2.13 GramNegative and GramPositive Bacteria

Gram-negative bacteria have an

extra membrane surrounding the

cell wall.





E. coli is a gram-negative bacterium, which means that it possesses two membranes. Outside the cytoplasmic membrane possessed by all cells are the cell wall and

a second, outer membrane (Fig. 2.13). (Although gram-negative bacteria do have two

compartments, they are nonetheless genuine prokaryotes, as their chromosome is in

the same compartment as the ribosomes and other metabolic machinery. They do not

have a nucleus, the key characteristic of a eukaryote). The presence of an outer

membrane provides an extra layer of protection to the bacteria. However, it can be

inconvenient to the biotechnologist who wishes to manufacture genetically engineered

proteins from genes cloned into E. coli. The outer membrane hinders protein secretion. Consequently there has been a recent upsurge of interest in gram-positive

bacteria, such as Bacillus, which lack the outer membrane.

Where Are Bacteria Found in Nature?

Familiar animals and plants

are vastly outnumbered by

microorganisms, in every

natural habitat.

Bacteria are found almost everywhere. Bacteria have been found 40 miles high in the

atmosphere and seven miles deep beneath the ocean floor. Some bacteria live in the

sea, others live in fresh water, and others are found growing happily in sewage. Some

bacteria live in the soil, some are found living in the roots of plants, and some live

inside animals. Most of the bacteria that live inside animals are harmless, and some are

even of positive value in aiding digestion or synthesizing vitamins that are absorbed

by their host animal.

The total number of bacteria on our planet is estimated at an unbelievable 5 ¥

1030. Over 90% are in the soil and subsurface layers below the oceans. The total amount

of bacterial carbon is 5 ¥ 1017 grams, nearly equal to the total amount of carbon found

in plants. Probably over half of the living matter on Earth is microbial.

In addition to the “normal” habitats, some bacteria live in extreme environments

where most other life forms cannot survive. Some bacteria can live in very concentrated salt solutions, such as the Dead Sea and the Great Salt Lake. Antarctic lakes

that only thaw for a short period of each year contain bacteria. Other bacteria inhabit

hot sulfur springs, where temperatures approach boiling point and the pH is close to

1. Bacteria even grow in some thermal deep sea vents where the temperature is above

100°C and the high pressure keeps the water liquid. Bacteria from these habitats may

gram-negative bacterium Type of bacterium that has both an inner (cytoplasmic) membrane plus an outer membrane which is located outside

the cell wall

gram-positive bacterium Type of bacterium that has only an inner (cytoplasmic) membrane and lacks an outer membrane


atients are usually given antibiotics to treat bacterial infections. These are

chemical substances capable of killing most bacteria by inhibiting specific

biochemical processes, but which are relatively harmless to people. The most

commonly used antibiotics, the penicillins and cephalosporins, are synthesized by

a kind of fungus known as mold (see Fig. 2.14). However, many antibiotics are

made by one kind of bacteria in order to kill other types of bacteria. The Streptomyces group of soil bacteria produces a wide range of antibiotics including

streptomycin, kanamycin and neomycin. Some antibiotics, like chloramphenicol,

were originally made by molds but nowadays can be chemically synthesized.

Finally, some antibiotics, such as sulfonamides, are entirely artificial and are only

synthesized by chemical corporations.

Mold naturally grows

on bread





Bacterial Growth Is Suppressed by Bread Mold

The blue mold that often grows on bread makes penicillin. When penicillin is produced by

molds grown on agar in a Petri dish, it will diffuse outwards and suppress the growth of

bacteria in a circle around it.

provide products that are useful because of their resistance to extreme conditions.

Thermus aquaticus, a bacterium from hot springs, has provided the heat stable DNA

polymerase needed for the polymerase chain reaction (PCR), a widely used technique

(see Ch. 23).

When different bacteria compete to live in the same habitat, they often resort to

biological warfare. Some bacterial strains secrete toxic chemicals in order to kill off

others that are competing for the same resources. Certain bacteria synthesize toxic proteins, known as bacteriocins. These proteins are designed to kill closely related bacterial strains, yet are harmless to the producer strain. Nisin, a bacteriocin produced by

some strains of Lactococcus lactis acts as a food preservative and kills food-borne

pathogens including Listeria monocytogenes and Staphylococcus aureus. Nisin and

related bacteriocins are relatively short peptides of molecular weight 3.5 kDa. They

are formed naturally by the strains of Lactococcus that are used to make silages and

fermented foods such as wara, a Nigerian cheese product, and kimchi (Korean traditional fermented vegetables). Although scientists have found relatively few practical

applications for bacteriocins, the plasmids which carry the genes for bacteriocins have

provided the most widely used vectors for carrying genes in genetic engineering

(described in Ch. 22).

Streptomycin and related antibiotics are also made by bacteria, especially those

of the Streptomyces group, to kill competing bacteria in the soil environment. These

antibiotics are not proteins (unlike the colicins) and have been widely used clinically.

antibiotics Chemical substances that inhibit specific biochemical processes and thereby stop bacterial growth selectively; that is, without killing

the patient too.

bacteriocin A toxic protein made by bacteria to kill other, closely related, bacteria

DNA polymerase An enzyme that elongates strands of DNA, especially when chromosomes are being replicated

penicillin An antibiotic made by a mold called Penicillium, which grows on bread producing a blue layer of fungus

PCR See polymerase chain reaction

vector (a) In molecular biology a vector is molecule of DNA which can replicate and is used to carry cloned genes or DNA fragments; (b) in

general biology a vector is an organism (such as a mosquito) that carries and distributes a disease-causing microorganisms (such as yellow fever

or malaria)

FIGURE 2.15 A Eukaryote

Has Multiple Cell


False color transmission electron

micrograph of a plasma cell from

bone marrow. Multiple

compartments surrounded by

membranes, including a nucleus,

are found in eukaryotic cells.

Characteristic of plasma cells is the

arrangement of heterochromatin

(orange) in the nucleus, where it

adheres to the inner nuclear

membrane. Also typical is the

network of rough endoplasmic

reticulum (yellow dotted lines) in the

cytoplasm. The oval or rounded

crimson structures in the cytoplasm

are mitochondria. Magnification

¥4,500. Provided by Dr. Gopal

Murti, Science Photo Library.

Some Bacteria Cause Infectious Disease,

but Most Are Beneficial

If higher organisms

disappeared from the Earth,

the prokaryotes would survive

and evolve. They do not need

us although we need them.

Bacteria are best known to the layman for causing infectious disease. Cholera, tuberculosis, bubonic plague (“Black Death”), anthrax, syphilis, gonorrhea, whooping cough,

diphtheria and a variety of other diseases are caused by bacteria. These diseases were

widespread before modern technology and hygiene largely eliminated them from

advanced societies. This was mostly due to clean water, sewers, flush toilets and soap,

rather than specifically “medical” advances such as the use of antibiotics or vaccinations.

Only a small proportion of bacteria causes disease. Many bacteria help maintain

the ecosystem by degrading waste materials. For example, soil bacteria degrade the

remains of dead plants and animals and take part in the breakdown of animal waste.

Bacteria also degrade many man-made chemicals and pollutants. If “good” bacteria

did not maintain the environment, higher life-forms could not survive.

Very occasionally bacteria which are even tinier than usual infect other, larger bacteria. This results in a bacterial disease of bacteria! The best known example of this is

Bdellovibrio bacterivorus. This penetrates the outer membrane of a wide range of

gram-negative bacteria, including E. coli, Pseudomonas, etc., and takes up residence in

the space between the inner and outer membranes. Bdellovibrio lives on nutrients it

steals from the host cell. After a few hours, the host cell bursts and releases half a dozen

new Bdellovibrio cells.

Eukaryotic Cells Are Sub-Divided into Compartments

A eukaryotic cell has its genome inside a separate compartment, the nucleus. In fact,

eukaryotic cells have multiple internal cell compartments surrounded by membranes

(Fig 2.15). The nucleus itself is surrounded by a double membrane, the nuclear envenuclear envelope

Envelope consisting of two concentric membranes that surrounds the nucleus of eukaryotic cells












A mitochondrion is surrounded by two concentric membranes. The inner membrane is folded inward

to form cristae. These are the site of the respiratory chain that generates energy for the cell.

Life is modular. Complex

organisms are subdivided into

organs. Large and complex

cells are divided into


lope, which separates the nucleus from the cytoplasm, but allows some communication

with the cytoplasm via nuclear pores (Fig 2.15). The genome of eukaryotes consists of

10,000–50,000 genes carried on several chromosomes. Eukaryotic chromosomes are

linear, unlike the circular chromosomes of bacteria. Most eukaryotes are diploid, with

two copies of each chromosome. Consequently, they possess at least two copies of each

gene. In fact, eukaryotic cells often have multiple copies of certain genes as the result

of gene duplication.

Eukaryotes possess a variety of other membranes and organelles. Organelles are

subcellular structures that carry out specific tasks. Some are separated from the rest of

the cell by membranes (so-called membrane-bound organelles) but others (e.g., the

ribosome) are not. The endoplasmic reticulum is a membrane system that is continuous with the nuclear envelope and permeates the cytoplasm. The Golgi apparatus is a

stack of flattened membrane sacs and associated vesicles that is involved in secretion

of proteins, or other materials, to the outside of the cell. Lysosomes are membranebound structures specialized for digestion, containing degradative enzymes.

All except a very few eukaryotes contain mitochondria (singular, mitochondrion;

Fig. 2.16). These are generally rod-shaped organelles, bounded by a double membrane.

They resemble bacteria in their overall size and shape. As will be discussed in more

detail (see Ch. 20), it is thought that mitochondria are indeed evolved from bacteria

that took up residence in the primeval ancestor of eukaryotic cells. Like bacteria, mitochondria each contain a circular molecule of DNA. The mitochondrial genome is

similar to a bacterial chromosome, though much smaller. The mitochondrial DNA has

some genes needed for mitochondrial function.

Mitochondria are specialized for generating energy by respiration and are found

in all eukaryotes. (A few eukaryotes are known that cannot respire; nonetheless these

retain remnant mitochondrial organelles—see below.) In eukaryotes, the enzymes of

respiration are located on the inner mitochondrial membrane, which has numerous

infoldings to create more membrane area. This contrasts with bacteria, where the respiratory chain is located in the cytoplasmic membrane, as no mitochondria are present.

crista (plural cristae) Infolding of the photosynthetic membrane in chloroplast

endoplasmic reticulum Internal system of membranes found in eukaryotic cells

Golgi apparatus A membrane bound organelle that takes part in export of materials from eukaryotic cells

lysosome A membrane bound organelle of eukaryotic cells that contains degradative enzymes

membrane-bound organelles Organelles that are separated from the rest of the cytoplasm by membranes

mitochondrion Membrane-bound organelle found in eukaryotic cells that produces energy by respiration

nuclear pore Pore in the nuclear membrane through which the nucleus communicates with the cytoplasm

organelle Subcellular structure that carries out a specific task. Membrane-bound organelles are separated from the rest of the cytoplasm by membranes but other organelles such as the ribosome are not.

Chloroplast outer





The chloroplast is bound by a

double membrane and contains

infolded stacks of membrane

specialized for photosynthesis. The

chloroplast also contains ribosomes

and DNA.





Chloroplasts are membrane-bound organelles specialized for photosynthesis

(Fig. 2.17). They are found only in plants and some single-celled eukaryotes. They are

oval to rod shaped and contain complex stacks of internal membranes that contain the

green, light-absorbing pigment chlorophyll and other components needed for trapping

light energy. Like mitochondria, chloroplasts contain a circular DNA molecule and are

thought to have evolved from a photosynthetic bacterium.

The Diversity of Eukaryotes

Unlike prokaryotes that fall into two distinct genetic lineages (the eubacteria and

archaebacteria), all eukaryotes are genetically related, in the sense of being ultimately

derived from the same ancestor. Perhaps this is not surprising since all eukaryotes

share many advanced features that the prokaryotes lack.When it is said that all eukaryotes are genetically related, it is in reference to the nuclear part of the eukaryotic

genome, not the mitochondrial or chloroplast DNA molecules that have become part

of the modern eukaryotic cell.

A wide variety of eukaryotes live as microscopic single cells. However, most

eukaryotes are larger multicellular organisms that are visible to the naked eye. Traditionally, these higher organisms have been divided into the plant, fungus and animal

kingdoms.This classification still holds, provided one remembers to include several new

groups to account for the single-celled eukaryotes. Some single-celled eukaryotes may

be viewed as plants, fungi or animals. Others are intermediate or possess a mixture of

properties and need their own miniature kingdoms.

Eukaryotes Possess Two Basic Cell Lineages

The most primitive multicellular organisms are merely aggregates of more or less identical cells. However, most multicellular organisms consist of distinct tissues and organs

containing a variety of specialized cells. Furthermore, most cells in higher organisms

do not contribute to the next generation, but die when the multicellular individual of

whom they are part dies. These are known as somatic cells (Fig. 2.20). Only the germ

line cells take part in forming a new individual. This, of course, complicates genetic

analysis. Although all cells in any multicellular organism start with an identical copy

of the genome, they differentiate to give quite different structures that perform different functions. Understanding development is a major challenge facing molecular

biology today. In animals there is a sharp division between somatic cells and germ line

cells that persists throughout the life cycle. However, plants do not set aside special

germ cells until close to the time that gametes are made.

germ line cells Reproductive cells producing eggs or sperm that take part in forming the next generation

chlorophyll Green pigment that absorbs light during photosynthesis

somatic cells Cells making up the body but which are not part of the germ cell line.

The Symbiotic Theory of Organelle Origins


branched off from the ancestral eukaryote before it

had captured the bacterium that gave rise to the mitochondrion. More recently, it was suggested that the

ancestors to these organisms did originally possess

mitochondria, but lost them secondarily during the

course of evolution. However, recent work has shown

that even Entamoeba and Giardia retain small remnant

organelles (“mitosomes”) corresponding to mitochondria. Although the capability for respiration has indeed

been completely lost, the remnant organelles function

in assembling the iron sulfur clusters found in several

essential proteins.

well accepted theory of mitochondrial (and

chloroplast) origin is that certain bacteria were

ingested by ancestral eukaryotes and have lived in a

symbiotic relationship with their descendents ever

since. Figure 2.18 suggests how this could have

occurred. The mitochondrion contains DNA and ribosomes. The DNA of the mitochondria more closely

resembles that of bacteria than of eukaryotes.

Certain primitive single-celled eukaryotes, such as

Entamoeba and Giardia, lack the ability to respire and

instead live by fermentation (Fig. 2.19). It was once

believed that they lacked mitochondria and had





inner outer





being engulfed


(now mitochondrion)

inside cell membrane















divides to

populate and

respire inside


Plants combining





Symbiosis with Respiring Bacteria Gives Rise to the Primitive

The ancestor to the eukaryote, or “urkaryote” engulfs a respiring bacterium by surrounding it with an

infolding of the cell membrane. Consequently there is now a double membrane around the newly

enveloped bacterium. The symbiont, now called a “mitochondrion”, divides by fission like a

bacterium and provides energy for the primitive eukaryote. The mitochondrion develops infoldings of

the inner membrane that increase its energy producing capacity.

Entamoeba A very primitive single-celled eukaryote that lacks mitochondria

fermentation A biochemical process that releases energy without oxygen or light

Giardia A very primitive single-celled eukaryote that lacks mitochondria

FIGURE 2.19 Entamoeba: an Anaerobic Eukaryote

Some single-celled eukaryotes lack true respiratory mitochondria and must grow by fermentation. Shown

here is a false-color transmission electron micrograph of Entamoeba histolytica, a parasitic amoeba, which

is ingesting human red blood cells (green ovals). The white/green oval (at left) with a blue and pink central

circular area is the nucleus. Entamoeba invades and destroys the tissues of the intestines, causing amoebic

dysentery. It may spread to the liver causing abscesses to develop. The infection is acquired through

contamination of food or water or through the agency of flies. Magnification: ¥830. Courtesy of: London

School of Hygiene & Tropical Medicine, Science Photo Library.

Organisms Are Classified

Biological classification

attempts to impose a

convenient filing system upon

organisms related by

continuous evolutionary


Living organisms have two names, both printed in italics; for example, Escherichia coli or

Saccharomyces cerevisiae. The first name refers to the genus (plural, genera), a group of

closely related species.After its first use in a publication,the genus name is often abbreviated to a single letter, as in “E. coli.” Next comes the species, or individual, name. The

genus and species are the smallest subdivision of the system of biological classification.

Classification of living organisms facilitates the understanding of their origins and the

relationships of their structure and function. The highest level of classification is the

domain. There are considered to be three domains:

1. Eubacteria These are prokaryotic cells (traditional bacteria). Interestingly, this

group includes the genomes of mitochondria and chloroplasts that have been

symbiotically related to eukaryotes.

2. Archaebacteria: From a structural viewpoint, these are prokaryotes like eubacteria in that they lack a nucleus. However, their gene sequences and other biochemical features indicate they are, if anything, slightly more closely related

genetically to eukaryotes than to eubacteria.

3. Eukaryotes: Higher organisms whose DNA is carried on several chromosomes

which are found inside the nucleus. Their cells are divided into separate compartments and usually contain other organelles in addition to the nucleus.

Eukaryotes are divided into four kingdoms:

Protoctista—An accumulation of primitive, mostly single-celled eukaryotes

often referred to as protists that don’t belong to the other three main kingdoms.

There are several groups that are distinct enough that some scientists would

elevate them in rank to miniature kingdoms.

domain (of life) Highest ranking group into which living creatures are divided, based on the most fundamental genetic properties

genus A group of closely related species

kingdom Major subdivision of eukaryotic organisms, in particular the plant, fungus and animal kingdoms



Destined to form

egg or sperm









Lives no longer

than individual

Liver cell


Somatic Cells versus Germ Line

After an egg is fertilized and begins its development into an animal embryo, cells have two fates. A

small number of cells form the germ line, which gives rise to the gametes (eggs or sperm) that give

rise to future generations. However, most cells are part of the somatic cell line, which forms the

remainder of the organism. These somatic cells will die either before the organism as a whole, or with

it, as part of the natural life cycle.









Plants—Possess both mitochondria and chloroplasts and are photosynthetic.

Typically they are non-mobile and have rigid cell walls made of cellulose.

Fungi—Possess mitochondria but lack chloroplasts. Once thought to be plants

that had lost their chloroplasts, it is now thought they never had them. Their

nourishment comes from decaying biomatter. Although fungi are non-mobile,

they lack cellulose and their cell walls are made of chitin. They may be more

closely related to animals than plants.

Animals—Lack chloroplasts but possess mitochondria. Differ from fungi and

plants in lacking a rigid cell wall. Typically mobile. They are divided into 20 to

30 phyla (singular, phylum), depending somewhat on personal taste. Some phyla



Cnidaria—sea anemones and jellyfish



Arthropoda—insects, crustaceans, etc.

Annelida—segmented worms, such as earthworms

Mollusca—snails, squids, etc.

phylum (plural phyla) Major groups into which animals are divided, roughly equivalent in rank to the divisions of plants or bacteria

Echinodermata—starfish, sea urchins

Chordata—vertebrates and their relatives.

Phyla are divided into classes, such as mammals.

Classes are divided into orders, such as primates.

Orders are divided into families, such as hominids.

Families are divided into genera, such as Homo.

Genera are divided into species, such as Homo sapiens

Some Widely Studied Organisms Serve as Models

Biologists have always concentrated their attention on certain living organisms, either

because they are convenient to study or are of practical importance. Inevitably,

model organisms are atypical in some respects. For example, few bacteria grow as

fast as E. coli and few mammals breed as fast as mice. Nonetheless, information

discovered in such model systems is assumed to apply also to related organisms. In practice this often proves to be true, at least to a first approximation. As discussed above,

the basic principles of molecular biology have been investigated in simple single-celled

prokaryotes. However, to obtain knowledge that is useful in medicine and agriculture,

researchers need model organisms that are much more closely related to humans and

to crop plants, respectively. Even these models have their limitations; ultimately, human

cells and agriculturally useful animals and plants have to be studied directly.

Yeast Is a Widely Studied Single-Celled Eukaryote

Biotechnology is a new word

but not a new occupation.

Brewing and baking both use

yeast and date back to the

earliest human civilizations.

Yeast is widely used in molecular biology for many of the same reasons as bacteria. It

is the eukaryote about which most is known and the first whose genome was

sequenced—in 1996. Yeasts are members of the fungus kingdom and are about equally

related to animals and plants. A variety of yeasts are found in nature, but the one normally used in the laboratory is brewer’s yeast, Saccharomyces cerevisiae (Fig. 2.21). This

is a single-celled eukaryote that is easy to grow in culture. Even before the age of

molecular biology, yeast was widely used as a source of material for biochemical analysis. The first enzymatic reactions were characterized in extracts of yeast and the word

enzyme is derived from the Greek for “in yeast”.

Although it is a “higher organism”, yeast measures up quite well to the list of useful

properties that make bacteria easy to study. In addition, it is less complex genetically

than many other eukaryotes:

a. Yeast is single-celled microorganism. Like bacteria, a yeast culture consists of

many identical cells. Although larger than bacteria, yeast cells are only about a

tenth the size of the cells of higher animals.

b. Yeast has a haploid genome of about 12 Mb of DNA with about 6,000 genes,

as compared to E. coli, which has 4,000 genes, and humans, who have approximately 25,000.

c. The natural life cycle of yeast alternates between a diploid phase and a haploid

phase. Thus it is possible to grow haploid cultures of yeast, which, like bacteria,

have only a single copy of each gene, making research interpretations easy.

d. Unlike many higher organisms, yeast has relatively few of its genes—about

5%—interrupted by intervening sequences, or introns.

e. Yeast can be grown under controlled conditions in chemically defined culture

medium and forms colonies on agar like bacteria.

f. Yeast grows fast, though not as fast as bacteria. The cell cycle takes approximately 90 minutes (compared to around 20 minutes for fast growing bacteria).

g. Yeast cultures can contain around 109 cells per ml of culture media, like



Yeast Cells

Colored scanning electron

micrograph (SEM) of budding yeast

cells (Saccharomyces cerevisiae).

The larger mother cells are budding

off smaller daughter cells.

Magnification: ¥4,000. Courtesy of:

Andrew Syred, Science Photo


h. Yeast can be readily stored at low temperatures.

i. Genetic analysis using recombination is much more powerful in yeast than in

higher eukaryotes. Consequently, collections of yeast strains that each have one

yeast gene deleted are available.

Yeast illustrates the genetic

characteristics of higher

organisms in a simplified



N + N












N + N





Yeast Life

The yeast cell alternates between

haploid and diploid phases and is

capable of growth and cell division

in either phase.

Yeast may grow as diploid or haploid cells (Fig. 2.22). Both haploid and diploid

yeast cells grow by budding, rather than symmetrical cell division. In budding, a bulge,

referred to as a bud, forms on the side of the mother cell. The bud gets larger and one

of the nuclei resulting from nuclear division moves into the bud. Finally, the cross wall

develops and the new cell buds off from the mother. Especially under conditions of

nutritional deprivation, diploid yeast cells may divide by meiosis to form haploid cells,

each with a different genetic constitution. This process is analogous to the formation

of egg and sperm cells in higher eukaryotes. However, in yeast, the haploid cells appear

identical and there is no way to tell the sexes apart and so we refer to mating types.

In contrast to the haploid gametes of animals and plants, the haploid cells of yeast may

grow and divide indefinitely in culture. Two haploid cells, of opposite mating types, may

fuse to form a zygote.

In its haploid phase, Saccharomyces cerevisiae has 16 chromosomes and nearly

three times as much DNA as E. coli. Despite this, it only has 1.5 times as many genes

as E. coli. Thus a substantial portion of yeast DNA apparently lacks genetic information and so is non-coding DNA. It is easier to use the haploid phase of yeast for isolating mutations and analyzing their effects. Nonetheless, the diploid phase is also

useful for studying how two alleles of the same gene interact in the same cell. Thus,

yeast can be used as a model to study the diploid state and yet take advantage of its

haploid phase for most of the genetic analysis.

A Roundworm and a Fly Are Model

Multicellular Animals

“If all the matter in the universe except the nematodes were swept

away, our world would still be dimly recognizable. . .”

—N.A. Cobb, 1914

Nematodes in oceanic mud or

inland soils may all look the

same. Nonetheless, they

harbor colossal genetic


Ultimately, researchers have to study multicellular creatures. The most primitive of

these that is widely used is the roundworm, Caenorhabditis elegans. Nematodes, or

roundworms, are best known as parasites both of animals and plants. Although it is

related to the “eelworms”—nematodes that attack the roots of crop plants—C. elegans,

is a free-living and harmless soil inhabitant that lives by eating bacteria. A single acre

budding Type of cell division seen in yeasts in which a new cell forms as a bulge on the mother cell, enlarges, and finally separates

non-coding DNA DNA sequences that do not code for proteins or functional RNA molecules


Caenorhabditis elegans

False-color scanning optical

micrograph of the soil-dwelling

bisexual nematode Caenorhabditis

elegans. The round internal

structures are eggs. C. elegans is

convenient for genetic analysis

because of its tendency to

reproduce by self-fertilization. This

results in offspring that are all

identical to the parent. It takes only

three days to reach maturity and

thousands of worms can be kept on

a culture plate. Approximate

magnification: ¥80C. Courtesy of:

James King-Holmes, Science Photo


of soil in arable land may contain as many as 3,000 million nematodes belonging to

dozens of different species.

The haploid genome of Caenorhabditis elegans consists of 97 Mb of DNA carried

on six chromosomes. This is about seven times as much total DNA as in a typical yeast

genome. C. elegans has an estimated 20,000 genes and so contains a much greater proportion of non-coding DNA than lower eukaryotes such as yeast. Its genes contain an

average of 4 intervening sequences each.

The adult C. elegans is about 1 mm long and has 959 cells and the lineage of each

has been completely traced from the fertilized egg (i.e., the zygote). It is thus a useful

model for the study of animal development. In particular, apoptosis, or programmed

cell death, was first discovered and has since been analyzed genetically using C. elegans.

Although very convenient in the special case of C. elegans, such a fixed number of cells

in an adult multicellular animal is extremely rare. C. elegans, which lives about 2–3

weeks, is also used to study life span and the aging process. RNA interference, a genesilencing technique that relies on double-stranded RNA, was discovered in C. elegans

in 1998 and is now used to study gene function during development in worms and other

higher animals. RNA interference is discussed in Ch. 11.

As noted in Chapter 1, the fruit fly, Drosophila melanogaster (usually called

Drosophila) was chosen for genetic analysis in the early part of the 20th century. Fruit

flies live on rotten fruit and have a 2 week life cycle, during which the female lays

several hundred eggs.The adults are about 3 mm long and the eggs about 0.5 mm. Once

molecular biology came into vogue it became worthwhile to investigate Drosophila at

the molecular level, in order to take advantage of the wealth of genetic information

already available. The haploid genome has 180 Mb of DNA carried on 4 chromosomes.

Although we normally think of Drosophila as more advanced than a primitive roundworm, it has an estimated 14,000 genes—6,000 fewer than the roundworm, C. elegans.

Genes from Drosophila contain approximately 3 intervening sequences each on

average. Research on Drosophila has concentrated on cell differentiation, development, signal transduction and behavior.

Zebrafish are used to Study Vertebrate Development

Danio rerio, (previously Brachydanio rerio) the zebrafish, is increasingly being used as

a model for studying genetic effects in vertebrate development. Zebrafish are native

to the slow freshwater streams and rice paddies of East India and Burma, including

the Ganges River. They are small, hardy fish, about an inch long that have been bred

apoptosis Programmed suicide of unwanted cells during development or to fight infection

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